Rapid and widespread emergence of antibiotic-resistant pathogens creates an urgent need for concerted approaches towards novel antibacterials. The long-term objective of this proposal is the development of synthetic antibiotics that overcome known resistance mechanisms. Structure-based molecular design in combination with leading-edge synthetic chemistry and screening methods will be used to exploit emerging structural data on the bacterial ribosome, a proven target for antibiotics. Selected natural antibiotics will serve as paradigms for the design of libraries consisting of novel aminoglycoside derivatives and thiopeptide mimetics. Crystal structures of the ribosomal target sites and computational analysis of their molecular recognition by ligands will aid the compound design effort. Compound libraries will be synthesized using convergent routes. Screening of compound libraries for their activity on the ribosomal target will be performed by fluorescence assays that have been developed for RNA targets at Anadys Pharmaceuticals. The integration of structure-based ligand design for the ribosome, one of the most complex macromolecular assemblies, with efficient synthesis of structurally complex ligands and their screening represents a formidable challenge. The benefit of the proposed research will extend beyond the immediate antibiotic discovery effort by providing the proof of principle for RNA as a feasible target for synthetic drugs. PROPOSED COMMERCIAL APPLICATIONS: The proposed research is aimed at discovering lead compounds that are potential antibiotics for the therapy of bacterial infections, especially for pathogens with resistance against existing antibiotics.